title: Efficient solvent boundary potential for hybrid potential simulations.
abstract: A common challenge in computational biophysics is to obtain statistical properties similar to those of an infinite bulk system from simulations of a system of finite size. In this work we describe a computationally efficient algorithm for performing hybrid quantum chemical/molecular mechanical (QC/MM) calculations with a solvent boundary potential. The system is partitioned into a QC region within which catalytic reactions occur, a spherical region with explicit solvent that envelops the quantum region and is treated with a MM model, and the surrounding bulk solvent that is treated implicitly by the boundary potential. The latter is constructed to reproduce the solvation free energy of a finite number of atoms embedded inside a low-dielectric sphere with variable radius, and takes into account electrostatic and van der Waals interactions between the implicit solvent and the QC and MM atoms in the central region. The method was implemented in the simulation program pDynamo and tested by examining elementary steps in the reaction mechanisms of two enzymes, citrate synthase and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated with the method and those obtained by previous experimental and computational studies. Directions in which the utility of the method can be further improved are discussed.
authors.affiliation: Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CEA, CNRS UMR5075, Université Joseph Fourier-Grenoble I), 41 rue Jules Horowitz, 38027 Grenoble, France.
authors.forename: Alexey
authors.initials: A
authors.lastname: Aleksandrov
authors.forename: Martin
authors.initials: M
authors.lastname: Field
mesh_terms: D000465:Algorithms; D055162:Biocatalysis; D002950:Citrate (si)-Synthase / Q000378:metabolism; D045022:Lactate Dehydrogenases / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*
chemical_list: D012997:Solvents; D045022:Lactate Dehydrogenases; D002950:Citrate (si)-Synthase